Barely Breathing
by MacGateFan
Summary: Takes place after Lifeline. Atlantis waits for the SGC to assign a new CO. Sheppard had temporarily replaced Elizabeth, but he realizes something now that it's too late. SW


Title: Barely Breathing

Rating: G

Author: MacGateFan

Disclaimers: All Stargate Atlantis characters belong to people who aren't me.

* * *

Prologue

He slips into her quarters unnoticed. He goes there every night. He walks around the room and talks to her. He knows she can't hear him but he doesn't care. As long as no one finds out he's fine. This is just something he has to do.

He sits on her bed and caresses the pillow, imagining her head lying on it as her hair spread around like a halo because she was an angel. She was his angel. She had swooped down from the heavens and brought him to Atlantis.

* * *

It had been nearly a month since they lost her on the Replicator homeworld and John Sheppard's nightmares were growing steadily worse. He no longer slept, merely moved around the city, making certain everyone was tucked safely in their beds. He might have even asked for some time off but the IOA was taking forever choosing someone to replace her.

Strike that, no one could ever replace her. She was Elizabeth Weir. She was everything to the Atlantis expedition. She was everything to him. There, he admitted it. Not only had she seen past his record enough to allow him to join the mission, she became his advocate when they were going to give Caldwell his job.

Elizabeth was the heart of Atlantis. She would, and did, do everything for those under her command. John always thought she'd make one helluva general.

John paused when he came to the balcony doors. Their balcony doors. With a deep breath, he thought them open and stepped into the warm night air. Both moons were shining brightly above the city. His eyes wondered over to the mainland and he idly wondered about those snakes Rodney mentioned. He only hoped they didn't like water and realized he should check into that.

He took a deep breath and closed his eyes, hands wrapped tightly around the balcony railing. "Elizabeth, you would love the view here. True it's not the same as our previous planet, but it's amazing."

John opened his eyes a few minutes later. He was glad no one had walked out while he was lost in thought a moment ago. He really didn't want the expedition team to think their current CO was off his rocker.

John decided he was going to try his hand at sleeping so he looked up at the moons and wished Elizabeth good night before heading back inside. By the time he made it to his quarters, he was ready to collapse onto his bed and did so without changing.

Before John knew it, someone was trying to get his attention. He grumbled then replied. "Go ahead."

_"Colonel,"_Chuck said, _"General Landry just dialed in. He'd like to speak to you."_

"I'm on my way."

John tried to make it up to the control room in five minutes, but he kept drifting off as he bent down to tie his shoes. Finally he got up and headed to the control room. "General Landry," he said with a nod, hoping he didn't look as tired as he felt.

_"Colonel Sheppard. I just wanted to inform you that the IOA finished with the reports and has sent Woolsey to discuss them with you at length. General O'Neill will be with him since he tends to keep the man tempered. They'll be there by the end of the week."_

John nodded. "Yes, Sir."

_"Oh, and Colonel? Get some sleep."_

"I will, Sir."

It had been two days since John talked to Landry and he had yet to fall asleep. He rubbed his eyes as he attempted to read the latest repair report. The asteroids had caused some significant damage to the outer edge of the city and construction was slow going for the team from Earth.

John made a decision and shut off the computer. He was going to attempt to get some sleep. If Woolsey saw how tired he was, it would only give the IOA more cause to get rid of him since Elizabeth...

John took a deep breath as he felt tears threatening to spill over. He would have to hold it together as he made his way to his quarters. He quickly told Chuck to call him if there were any problems then rushed out of the control room. John could feel all eyes on him but he ignored everyone and finally made it to his quarters.

He had a few sleeping pills stashed in his room from the other day when he had seen Dr. Keller. He knew she was just trying to help and maybe taking them would give him the much-needed sleep he craved so much.

John knew there was one person who wouldn't judge him about taking the pills. "Teyla, come in."

_"Go ahead, John."_

"I'm going to try and take some of these sleeping pills, could you keep an eye on things for me?"

_"Of course. I will notify you if there is something that needs your immediate attention."_

"Thanks."

_"You are welcome, John."_

With that out of the way, John took the pills, washing them down with some water. He removed his radio and lay down. Sleep came to him the moment his head hit the pillow.

* * *

Rodney had looked everywhere for John, but the man was AWOL. He arrived at the top of the control room stairs expecting to see his friend lounging in Elizabeth's old office. Rodney paused in his thought process then shook his head. Instead of John, he saw Teyla.

"Hey," he said. "Have you seen Sheppard? He was supposed to meet me in my lab this afternoon and he hasn't answered my calls."

Teyla nodded. "Colonel Sheppard is resting in his quarters per Dr. Keller's orders, Rodney. You will just have to wait until later to speak with him."

Rodney sighed. He had been waiting all week for John. "We really need to run a diagnostic on the weapon's chair. We may have burned it out."

"I am certain there are other people with the ATA gene who could help you with that just for now," Teyla replied. "John needs his rest. He is not taking losing Elizabeth very well."

"Do you think any of us are?" Rodney asked in irritation.

She shook her head. "I did not mean it that way, Rodney. What I am saying is that this has hit John harder than any of us. He feels more than anyone I have ever met but he never lets those feelings out for fear it would hurt more."

"What are you saying?" Teyla merely gave him a look because he knew exactly what she meant. "I never even thought about it, but now that you mention it. Oh God, he was in love with her, wasn't he?"

* * *

Rodney knew Teyla would kick his ass if she knew what he was doing, but he had to check on his friend. Now that he thought back through the last few years, he realized it had happened right in front of him so many times.

From John's scream at Kolya when he thought Elizabeth was dead to the look on Elizabeth's face when John was sacrificing himself to save them all from the Wraith. He heard about that hug in the middle of the Gateroom. A hug that everyone thought was going to be a kiss.

When John didn't answer the door, Rodney fiddled with the crystals and in two minutes, he was in his friend's quarters. "Sheppard," he whispered.

John stirred and turned to face Rodney, but didn't wake up. He said something but Rodney had to strain to hear it. "'Night Elizabeth."

Damn it! Rodney thought. "This was so unfair! Why did Elizabeth have to be the one? How can fate be so cruel as to take the one person who held this expedition together? What did she ever do to anyone?"

"That's what I keep asking myself, Rodney."

Rodney blinked, not surprised that John was awake, but that he was speaking out loud. "I'm sorry. I didn't mean to wake you."

"It's all right," John said with a sigh as he thought the lights on. "I wasn't fully asleep anyway. Those damn pills did nothing for me."

"Wow, you should see Keller. You look like night of the living dead!"

John glared at him. "Thanks, Rodney, that was so sweet."

"Well you do!" Rodney was about to say more when he heard a beep in his ear. "This better be good."

"Rodney I hope you're not disturbing Colonel Sheppard."

"To be honest, Dr. Keller, I am. However it's not my fault. The man looks like death warmed over and the sleeping pills you gave him aren't working. We'll be there in ten minutes."

"You'd better be or I'll send Ronon after you."

"What the hell was that for?" John asked.

This time is was Rodney's turn to glare. "I, for one, do not want to be dragged out of your quarters by Ronon, do you?"

* * *

"Colonel, why didn't you come to me sooner?" John merely shrugged in response. Jennifer was finding it increasingly disconcerting that he seemed so passive lately. And what made it worse was that she missed the signs.

Jennifer continued to check his vitals, noting that he was slightly hypertensive and his skin color seemed almost gray. She remembered the few hours after John had landed the city. When he came to check on Elizabeth's condition he seemed tired, but Jennifer had been so concerned with her more critical patient, she didn't think of anything else.

John closed his eyes as a wave of dizziness assailed him. He had never had it that bad before. After he took a deep breath to calm himself, John opened his eyes to find himself lying on his back. "Doc?"

"Just relax, Colonel. I'm going to give you something to help you sleep so don't fight. I know how much you want to stay awake, but if you do, you'll only hurt yourself."

John nodded as he drifted off, too exhausted to argue. "K, Doc."

Once he was out, Jennifer sighed. She had seen sleep deprivation before but never to this extent. She wasn't a pyschologist, but she knew that John was subconsciously keeping himself awake for fear of the nightmares.

Now they just had to make certain he was well rested for his meeting with Woolsey and O'Neill. From what she gathered from his team, if Sheppard had to be transferred back to Earth, it wouldn't go over well.

Jennifer knew that he had to stay. The expedition needed him as much as he needed them. Once she had made John comfortable, she'd give each of his friends time to sit with him. When the sleep meds wore off, the dreams would come back with a vengeance.

* * *

He glanced to his right and sat up when he saw her. She was just staring at him, an unreadable expression on her face. John placed his barefeet onto the cold, hard floor of the infirmary, quietly stepping towards her.

"Elizabeth?"

"I loved you, John," she finally said after a moment. "You said you would never leave anyone behind and you left me! Me, John!"

"I'm-I'm sorry, Elizabeth. I never meant to... I didn't mean..."

Elizabeth tilted her head mockingly at him. "Didn't mean to? John, you sound like a child. Quit begging for forgiveness because you are never going to get it! The SGC will see how careless and unreliable you are, just as I have."

John stepped closer, reaching out for her, but before he could, she was gone. "No, please, Elizabeth!"

Rodney nearly dropped his laptop when he heard John cry out. He immediately stood up, and took John's hand. "John, wake up! John!"

John blinked in confusion, which wore off the minute he saw he was in the infirmary and Rodney was next to him. "Rodney."

"Hey. You okay?"

"Do I look okay?"

He shrugged. "Not 100 percent. You look better than you did 12 hours ago."

"So I guess I was finally able to get some sleep, huh?"

"It seems like it," Rodney replied. "Although I doubt that 12 hours isn't going to please Dr. Keller. Do you want to talk about it?"

John eyed Rodney cautiously. "What?"

"Don't play dumb with me, Sheppard," Rodney said.

John took a deep breath. He was about to admit out loud how he really felt about Elizabeth and that he really was useless and unreliable. "When I close my eyes I see her, Rodney. She's so angry at me. She tells me she hates me and that I'm..."

"You're what?"

"Unreliable."

"I don't think so, John."

"Why do you say that?" John asked, clearly confused.

Rodney gave him a look that said, 'Are you really asking that?' "Because you have been the most reliable person on this expedition, well besides me of course. You are constantly making sure no one is left behind. You are constantly there to help everyone else even when you're injured. Trust me, you are the most reliable person I know!"

"I suppose."

"Sheppard, snap out of it! What you went through in that dream was just that. A dream plus guilt that's eating you up inside. Well, from what Ronon told me, you wanted to help her but she ordered you to leave. She sacrificed herself for us, John. For you! Because she loved you just as much as you loved her. Don't discount that sacrifice. Elizabeth doesn't deserve that!"

John stared at Rodney, mouth slightly open. "Wow, Rodney."

"Yeah, but it's true."

"It is," John replied. "I think I'm going to try and sleep again. Thanks."

"Anytime."

Rodney began talking about something else, but John was still exhausted so he immediately drifted off to sleep again and in his dreams, he saw her...

"You really should listen to Rodney more often," Elizabeth said, turning to face him.

John was taken aback by how beautiful she looked. She was still in her base uniform, but there was something about her. He hesitantly moved closer and when she didn't say anything, John moved so he was standing five feet in front of her.

"Elizabeth."

She smiled, reaching up to touch his cheek. "John, I want you to know that I don't blame you. After all, it was my decision, wasn't it? You would have done the same."

"I know that now and I'm sorry I was being so selfish. You did what you had to do and I was so angry at myself for not being able to protect you because I... I love you, Elizabeth."

"I love you too, John. And you know that deep down inside that I'm not just telling you these things because I'm your consciousness. I'm telling you because it's true. Elizabeth Weir loves you so deeply."

When John woke up, he felt more refreshed than he had in months. According to Dr. Keller he had been asleep, waking up in small spurts, for nearly 48 hours. She was beginning to see much improvement and John was able to sit up and eat without falling asleep.

As he ate his soup, he heard footsteps. He looked up to see Dr. Keller. "Hey, Doc."

"How are you feeling, Colonel?"

"Much better, thanks... um, what's going on with Woolsey and O'Neill?"

"They had their meeting with Dr. McKay and Major Lorne," Dr. Keller replied. He saw the worried expression on his face. "Don't worry, they understand the situation. Especially General O'Neill apparently. Anyway, they're still here and want to speak to you about what happened whenever you're ready."

John nodded. "If it's all right with you, I'm ready now. We need to get back out there and find Elizabeth."

"I couldn't agree more, Colonel Sheppard."


End file.
